Fix overlapping in conda enviroment creation when equivalent but diff…

…erent relative paths

Signed-off-by: jorgee <[email protected]>

modules/nextflow/src/main/groovy/nextflow/conda/CondaCache.groovy

@@ -359,8 +359,8 @@ class CondaCache {
      *      The {@link DataflowVariable} which hold (and pull) the local image file
      */
     @PackageScope
-    DataflowVariable<Path> getLazyImagePath(String condaEnv) {
-
+    DataflowVariable<Path> getLazyImagePath(String rawCondaEnv) {
+        def condaEnv = normalizeCondaEnv(rawCondaEnv)
         if( condaEnv in condaPrefixPaths ) {
             log.trace "${binaryName} found local environment `$condaEnv`"
             return condaPrefixPaths[condaEnv]
@@ -399,4 +399,12 @@ class CondaCache {
         return result
     }
 
+    String normalizeCondaEnv(String rawCondaEnv) {
+        // Check if it's a path (as in getPrefixPath)
+        if( !isYamlUriPath(rawCondaEnv) && ( isYamlFilePath(rawCondaEnv) || isTextFilePath(rawCondaEnv) || rawCondaEnv.contains('/') ) ) {
+            final path = rawCondaEnv as Path
+            return path.toAbsolutePath().normalize().toString()
+        }
+        return rawCondaEnv
+    }
 }

modules/nextflow/src/test/groovy/nextflow/conda/CondaCacheTest.groovy

@@ -569,4 +569,21 @@ class CondaCacheTest extends Specification {
         cleanup:
         folder?.deleteDir()
     }
+
+    def 'should normalize paths' () {
+
+        given:
+        def cache = new CondaCache()
+
+        expect:
+            cache.normalizeCondaEnv(RAW_CONDA_ENV) == EXPECTED
+
+        where:
+        RAW_CONDA_ENV                   | EXPECTED
+        'bwa=1.1.1'                     | 'bwa=1.1.1'
+        'http://url.com/path/env.yml'   | 'http://url.com/path/env.yml'
+        '/path/to/../directory'         | '/path/directory'
+        '/path/./to/file.txt'           | '/path/to/file.txt'
+        '/path/./to/file.yml'           | '/path/to/file.yml'
+    }
 }